Added FunctionVariant draft to schema/cat-vrs/recipe-source.yml, whic…

…h also involved added drafting FunctionConstraint and GeneContextConstraint to schema/cat-vrs/def and schema/cat-vrs/json.

schema/cat-vrs/def/FunctionConstraint.rst

@@ -0,0 +1,33 @@
+.. note:: This data class is at a **draft** maturity level and may \
+    change in future releases. Maturity \
+    levels are described in the :ref:`maturity-model`.
+
+**Computational Definition**
+
+A categorical label of the function change that members of this categorical variant satisfies.
+
+**Information Model**
+
+Some FunctionConstraint attributes are inherited from :ref:`Constraint`.
+
+.. list-table::
+    :class: clean-wrap
+    :header-rows: 1
+    :align: left
+    :widths: auto
+
+   *  - Field
+      - Flags
+      - Type
+      - Limits
+      - Description
+   *  - type
+      -
+      - string
+      - 1..1
+      - MUST be "FunctionConstraint"
+   *  - functionConsequence
+      -
+      - string
+      - 1..1
+      - A categorical label of the function change that members of this categorical variant satisfies, using ontology terms from [The Sequence Ontology](http://www.sequenceontology.org).

schema/cat-vrs/def/GeneContextConstraint.rst

@@ -0,0 +1,33 @@
+.. note:: This data class is at a **draft** maturity level and may \
+    change in future releases. Maturity \
+    levels are described in the :ref:`maturity-model`.
+
+**Computational Definition**
+
+A free-text description of the gene context that members of this categorical variant satisfies.
+
+**Information Model**
+
+Some FunctionConstraint attributes are inherited from :ref:`Constraint`.
+
+.. list-table::
+    :class: clean-wrap
+    :header-rows: 1
+    :align: left
+    :widths: auto
+
+   *  - Field
+      - Flags
+      - Type
+      - Limits
+      - Description
+   *  - type
+      -
+      - string
+      - 1..1
+      - MUST be "GeneContextConstraint"
+   *  - geneContext
+      -
+      - string
+      - 1..1
+      - A gene identifier.

schema/cat-vrs/json/FunctionConstraint

@@ -0,0 +1,37 @@
+{
+   "$schema": "https://json-schema.org/draft/2020-12/schema",
+   "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/FunctionConstraint",
+   "title": "FunctionConstraint",
+   "type": "object",
+   "maturity": "draft",
+   "description": "A categorical label of the function change that members of this categorical variant satisfies.",
+   "properties": {
+      "type": {
+         "type": "string",
+         "const": "FunctionConstraint",
+         "default": "FunctionConstraint",
+         "description": "MUST be \"FunctionConstraint\""
+      },
+      "functionConsequence": {
+         "description": "A categorical label of the function change that members of this categorical variant satisfies, using ontology terms from [The Sequence Ontology](http://www.sequenceontology.org). ``SO:0002052`` refers to a [dominant negative variant](http://www.sequenceontology.org/browser/current_release/term/SO:0002052), a variant where the mutated gene product adversely affects the other (wild type) gene product. ``SO:0002054`` refers to a [loss of function variant](http://www.sequenceontology.org/browser/current_release/term/SO:0002054), a sequence variant whereby the gene product has diminished or abolished function. ``SO:0001561`` refers to a [polypeptide partial loss of function](http://www.sequenceontology.org/browser/current_release/term/SO:0001561), a sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence. ``SO:0002219`` refers to a [functionally normal](http://www.sequenceontology.org/browser/current_release/term/SO:0002219) variant, a sequence variant in which the function of a gene product is retained with respect to a reference. ``SO:0001557`` refers to a [polypeptide gain of function variant](http://www.sequenceontology.org/browser/current_release/term/SO:0001557), a sequence variant which causes gain of polypeptide function with respect to a reference sequence. ``SO:0002053`` refers to a [gain of function variant](http://www.sequenceontology.org/browser/current_release/term/SO:0002053), a sequence variant whereby new or enhanced function is conferred on the gene product.",
+         "type": "string",
+         "enum": [
+            "SO:0002052",
+            "SO:0002054",
+            "SO:0001561",
+            "SO:0002219",
+            "SO:0001557",
+            "SO:0002053
+         ]
+      },
+      "description": {
+          "description": "A free-text description of the function change.",
+          "type": "string"
+      }
+   },
+   "required": [
+      "functionConsequence",
+      "type"
+   ],
+   "additionalProperties": false
+}

schema/cat-vrs/json/GeneContextConstraint

@@ -0,0 +1,41 @@
+{
+   "$schema": "https://json-schema.org/draft/2020-12/schema",
+   "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/GeneContextConstraint",
+   "title": "GeneContextConstraint",
+   "type": "object",
+   "maturity": "draft",
+   "description": "A free-text description of the gene context that members of this categorical variant satisfies.",
+   "properties": {
+      "type": {
+         "type": "string",
+         "const": "GeneContextConstraint",
+         "default": "GeneContextConstraint",
+         "description": "MUST be \"GeneContextConstraint\""
+      },
+      "geneContext": {
+         "description": "A gene identifier",
+         "type": "string"
+      },
+      "description": {
+          "description": "A free-text description of the gene context.",
+          "type": "string"
+      },
+      "relations": {
+         "type": "array",
+         "ordered": false,
+         "items": {
+            "type": string,
+            "enum": [
+               "genome_liftover",
+               "transcript_projection"
+            ]
+         },
+         "description": "Defined relationships from which members relate to the defining location. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. \"GRCh37\" and \"GRCh38\") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept."
+      }
+   },
+   "required": [
+      "geneContext",
+      "type"
+   ],
+   "additionalProperties": false
+}

schema/cat-vrs/recipes-source.yaml

@@ -86,4 +86,25 @@ $defs:
                 - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint"
                 - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint"
         required:
-          - constraints
+          - constraints
+
+  FunctionVariant:
+    maturity: draft
+    description: >-
+      A representation of the constraints for matching knowledge about function variants; e.g., gain-of-function or
+      loss-of-function.
+    allOf:
+      - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant"
+      - properties:
+          constraints:
+            description: >-
+              The constraints array must contain exactly two items:
+              a GeneContextConstraint and a FunctionConstraint.
+            minItems: 2
+            maxItems: 2
+            contains:
+              allOf:
+                - $ref: "/ga4gh/schema/cat-vrs/1.x/json/GeneContextConstraint"
+                - $ref: "/ga4gh/schema/cat-vrs/1.x/json/FunctionConstraint"
+        required:
+          - constraints